Contacts of the helix formed by residues 151 - 167 (chain A) in PDB entry 1EBM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ASN* 1.3 80.3 + - - +
152A ILE* 1.3 66.6 + - - +
153A ALA* 3.3 12.9 + - + +
154A ARG* 2.8 39.4 + - - +
155A ILE* 2.9 24.4 + - - +
24C A 3.4 45.1 + - - +
25C 8OG 4.0 1.6 - - - +
10D T 4.8 1.4 + - - -
11D G 4.2 11.3 + - - +
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Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PRO 4.1 15.9 - - - +
41A SER 4.2 0.7 - - - +
42A GLY* 4.0 15.3 - - - +
45A PHE* 4.1 19.7 - - + -
151A ASN* 1.3 71.7 - - - +
153A ALA* 1.3 58.7 + - - +
155A ILE* 3.7 8.4 - - + +
156A THR* 2.7 43.2 + - - +
319A PHE* 4.6 4.9 - - + -
323A LEU* 3.7 36.1 - - + -
25C 8OG 2.9 37.7 + - - +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG* 5.6 0.7 + - - -
151A ASN* 3.1 10.6 + - - +
152A ILE* 1.3 82.0 - - - +
154A ARG* 1.3 61.9 + - - +
156A THR* 3.4 12.1 + - - -
157A GLY* 3.4 8.8 + - - -
12D G 6.4 2.7 - - - -
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASN 4.9 0.6 + - - -
150A ASN* 3.0 29.2 + - - +
151A ASN* 2.8 22.8 + - - +
153A ALA* 1.3 70.1 - - - +
155A ILE* 1.3 67.6 + - - +
157A GLY* 3.0 12.4 + - - -
158A MET* 3.0 40.0 + - - +
161A ARG* 5.1 4.7 + - - +
200A GLY 3.1 23.7 + - - -
204A ARG* 3.8 9.7 - - - +
9D C 2.7 41.2 + - - +
10D T 2.9 46.3 + - - +
11D G 4.5 21.1 - - - +
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.4 39.0 - - + -
143A SER 4.3 12.6 - - - +
146A CYS* 4.4 3.8 - - + +
147A SER* 3.7 34.3 - - - +
150A ASN* 3.7 25.1 + - + +
151A ASN 2.9 31.4 + - - +
152A ILE* 3.7 8.3 - - - +
154A ARG* 1.3 75.7 - - - +
156A THR* 1.3 64.1 + - - +
158A MET* 3.2 6.3 + - - +
159A VAL* 3.0 27.9 + - + +
25C 8OG 4.2 7.6 - - + +
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.6 38.4 - - - +
47A TRP 5.7 1.8 - - - +
48A ARG* 3.4 38.6 - - - +
152A ILE* 2.7 28.3 + - - +
153A ALA* 3.5 7.5 - - - -
154A ARG 3.2 0.2 - - - -
155A ILE* 1.3 77.6 - - - +
157A GLY* 1.3 61.5 + - - +
159A VAL* 3.5 2.6 + - - +
160A GLU* 3.1 25.1 + - - +
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ARG* 4.8 2.9 - - - +
153A ALA 3.4 5.5 + - - -
154A ARG* 3.0 7.5 + - - -
156A THR* 1.3 75.9 - - - +
158A MET* 1.3 66.0 + - - +
160A GLU* 3.1 13.2 + - - +
161A ARG* 2.9 44.8 + - - +
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Residues in contact with MET 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A CYS* 3.7 35.7 - - + +
150A ASN* 3.2 23.8 - - - +
154A ARG* 3.0 36.4 + - - +
155A ILE* 3.5 7.2 - - - +
157A GLY* 1.3 75.1 - - - +
159A VAL* 1.3 59.6 + - - +
161A ARG* 3.3 18.5 + - - +
162A LEU* 2.9 30.4 + - - +
200A GLY 4.0 3.4 - - - +
201A LEU* 3.3 54.4 - - + +
204A ARG* 4.2 6.5 - - - +
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 4.5 14.1 - - + +
46A ARG* 3.9 29.6 - - + -
143A SER* 4.0 36.3 - - - +
146A CYS* 4.5 10.8 - - + -
155A ILE* 3.0 32.2 + - + +
156A THR 3.9 3.6 - - - +
158A MET* 1.3 76.0 - - - +
160A GLU* 1.3 58.0 + - + +
162A LEU* 3.4 7.9 + - + +
163A CYS* 3.0 32.0 + - - -
181A PHE* 4.4 5.8 - - + -
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Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE 5.1 6.2 - - - +
46A ARG* 5.9 8.2 - - - +
48A ARG* 2.7 51.3 + - - +
156A THR* 3.1 17.4 + - + +
157A GLY* 3.1 12.1 + - - +
159A VAL* 1.3 75.6 - - + +
161A ARG* 1.3 62.0 + - + +
163A CYS* 3.3 6.4 + - - +
164A GLN* 3.0 29.4 + - - +
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 5.1 4.2 + - - +
157A GLY* 2.9 33.7 + - - +
158A MET* 3.7 27.0 - - - +
160A GLU* 1.3 74.9 - - + +
162A LEU* 1.3 63.9 + - - +
164A GLN* 3.9 6.1 - - - +
165A ALA* 3.0 27.5 + - - +
199A LEU* 2.8 59.7 + - + +
200A GLY* 4.4 5.9 + - - -
201A LEU* 5.6 0.2 - - + -
11D G 5.8 1.6 + - - -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PHE* 5.3 5.6 - - + -
146A CYS* 4.5 11.2 - - - -
158A MET 2.9 17.5 + - - +
159A VAL* 3.6 7.9 - - + +
161A ARG* 1.3 78.8 - - - +
163A CYS* 1.3 61.2 + - - +
165A ALA* 4.8 0.9 - - - -
166A PHE* 3.1 26.3 + - + -
181A PHE* 4.1 17.0 - - + -
182A PRO* 3.4 31.8 - - + +
187A LEU* 4.4 9.2 - - + -
196A LEU* 4.4 22.7 - - + -
199A LEU* 4.7 0.8 - - - +
201A LEU* 4.2 20.4 - - + +
208A VAL* 4.3 22.9 - - + -
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Residues in contact with CYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ARG* 3.6 34.3 - - - +
159A VAL 3.0 21.2 + - - +
160A GLU* 3.3 4.9 + - - +
162A LEU* 1.3 75.8 - - - +
164A GLN* 1.3 61.1 + - - +
167A GLY* 2.7 28.8 + - - -
179A HIS* 3.4 12.2 - - + +
180A GLY 3.9 6.5 - - - +
181A PHE* 3.6 33.7 - - - -
182A PRO* 3.7 15.5 - - - -
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Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLU 3.0 16.6 + - - +
161A ARG* 3.9 6.7 - - - +
163A CYS* 1.3 78.1 - - - +
165A ALA* 1.3 62.1 + - - +
167A GLY 4.4 1.9 - - - +
179A HIS* 3.5 38.1 + - + +
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ARG 3.0 18.3 + - - +
164A GLN* 1.3 79.8 - - - +
166A PHE* 1.3 84.1 + - + +
167A GLY 5.3 0.2 - - - -
195A HIS* 4.2 13.9 + - + +
199A LEU* 3.8 17.5 - - + -
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 3.1 16.2 + - + +
165A ALA* 1.3 94.6 - - + +
167A GLY* 1.3 62.9 + - - +
168A PRO* 4.4 1.7 - - - +
182A PRO* 3.7 24.4 - - + +
183A SER 4.7 0.2 + - - -
186A ALA* 3.9 32.0 - - + +
187A LEU* 4.5 9.6 - - + -
192A VAL* 3.9 29.6 - - + -
195A HIS* 3.6 37.2 - + + -
196A LEU* 3.8 27.1 - - + -
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Residues in contact with GLY 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A CYS 2.7 23.4 + - - +
164A GLN 4.4 1.6 - - - +
165A ALA 5.3 0.2 - - - -
166A PHE* 1.3 76.6 - - - +
168A PRO* 1.3 75.5 - - - +
169A ARG 3.5 0.7 + - - -
179A HIS* 3.0 15.1 + - - -
180A GLY 3.3 11.2 - - - -
182A PRO* 3.7 7.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il